This page of the tool shed wiki has most of the details. The tool dependency
tag definitions are evolving rapidly as more tools are being included in the
Galaxy tool migration process. I'm trying to keep information updated, but at
times the wiki page will lag due to resource deficiencies.
ht
Dave,
Thanks for that, will pull the latest version and give it a go..
Is there any documentation on these tags and flags??? (tool dependencies
installation)
Cheers,
Franco
On 12/12/12 10:27 PM, "Dave Bouvier" wrote:
> Franco,
>
> I see the issue, the target_file flag was introduced in
>
Franco,
I see the issue, the target_file flag was introduced in
8268:87828175dfe7. If you update to the latest Galaxy dist release, that
tool dependency xml should work just fine.
--Dave B.
On 2012-12-12 01:53, Franco Caramia wrote:
Dave,
It's :
hg log | head
changeset: 8153:5dcbbdfe10
Dave,
It's :
hg log | head
changeset: 8153:5dcbbdfe1087
tag: tip
user:Daniel Blankenberg
date:Tue Nov 06 12:57:23 2012 -0500
summary: Allow rerun to access hidden datasets.
Thanks,
Franco
On 12/12/12 3:13 PM, "Dave Bouvier" wrote:
> Franco,
>
> You're right,
Franco,
You're right, I see a both clean and all rules in the makefile. It looks
almost like it's not finding the expected makefile, I'll have to look
into that in the morning. As for the download_by_url action, it
downloads and extracts the specified file, then changes to the extracted
direc
Hi Dave,
It does not require it, but it should not fail either as the clean rule is
in the makefile..
By removing it I get:
make: *** No rule to make target `all'. Stop.
Same problem as before but this time with the 'all' rule...
I'm not sure what the wrote:
> Franco,
>
> BEDTools, unlike some
Franco,
BEDTools, unlike some other packages, does not require the 'make clean'
shell command to compile. If you remove that line, the dependency should
install without problems.
--Dave B.
On 2012-12-11 21:16, Franco Caramia wrote:
Hi list,
I got the following tool_dependencies.xml file f
Hi list,
I got the following tool_dependencies.xml file failing:
http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz
make clean
make all
bin
$INSTALL_DIR/bin
$INSTALL_DI
R/bin
